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USGS2005

Biology and invasive species in the western U.S

The diversity of environments that characterizes the West is responsible for the region's rich biological heritage. This ecological diversity also means that opportunities for invasive species are many, varied, and complex. Island ecosystems are notoriously vulnerable to invaders as demonstrated in Hawaii and West Coast offshore islands. Aquatic invaders impose high economic and environmental costs in systems as varied as San Francisco Bay and desert springs in the Great Basin. Although the West's arid and montane ecosystems may seem resistant to plant and animal invaders, we now know that ex-otic species have altered physical processes related to fire and hydrology in a manner favoring further expansion and persis-tence of invaders. Natural resource managers value analytical, mapping, and genetics tools developed by USGS scientists to monitor invasive species and help conserve biological systems. USGS biologists conduct research to assist land and water managers' efforts to control invasive species and restore natural systems. Throughout the West, the USGS carries out studies for early detection and rapid assessment of invaders. The following are some examples of how the USGS is making a difference in the western United States.

Fact Sheet↗

USGS2024

Comparing modern identification methods for wild bees: Metabarcoding and image-based morphological taxonomic assignment

With the decline of bee populations worldwide, studies determining current wild bee distributions and diversity are increasingly important. Wild bee identification is often completed by experienced taxonomists or by genetic analysis. The current study was designed to compare two methods of identification including: (1) morphological identification by experienced taxonomists using images of field-collected wild bees and (2) genetic analysis of composite bee legs (multiple taxa) using metabarcoding. Bees were collected from conservation grasslands in eastern Iowa in summer 2019 and identified to the lowest taxonomic unit using both methods. Sanger sequencing of individual wild bee legs was used as a positive control for metabarcoding. Morphological identification of bees using images resulted in 36 unique taxa among 22 genera, and >80% of Bombus specimens were identified to species. Metabarcoding was limited to genus-level assignments among 18 genera but resolved some morphologically similar genera. Metabarcoding did not consistently detect all genera in the composite samples, including kleptoparasitic bees. Sanger sequencing showed similar presence or absence detection results as metabarcoding but provided species-level identifications for cryptic species (i.e., Lasioglossum ). Genus-specific detections were more frequent with morphological identification than metabarcoding, but certain genera such as Ceratina and Halictus were identified equally well with metabarcoding and morphology. Genera with proportionately less tissue in a composite sample were less likely to be detected using metabarcoding. Image-based methods were limited by image quality and visible morphological features, while genetic methods were limited by databases, primers, and amplification at target loci. This study shows how an image-based identification method compares with genetic techniques, and how in combination, the methods provide valuable genus- and species-level information for wild bees while preserving tissue for other analyses. These methods could be improved and transferred to a field setting to advance our understanding of wild bee distributions and to expedite conservation research.

PLoS ONE↗

USGS2003

Genetic comparison of lake sturgeon populations: Differentiation based on allelic frequencies at seven microsatellite loci

The lake sturgeon (Acipenser fulvescens) has recently become a high priority for restoration management because of the near extinction of the species from many areas of North America. The identification of the level of population differentiation that naturally exists among lake sturgeon populations will be useful in the development of management plans to conserve and restore diversity, and in the choice of donor populations to use for re-introduction. Genetic variation among and within 210 lake sturgeon collected from seven locations (St. Lawrence River, Des Prairies River (tributary to the St. Lawrence River), Mattagami River (Hudson Bay drainage), Menominee River (Lake Michigan drainage), Wolf River (Lake Michigan drainage), Niagara River, and Lake Erie) was examined based on allelic variation at seven microsatellite loci (four disomic and three putative tetrasomic). High levels of variability were detected at these loci. Analyses revealed an average of 8.6 alleles per locus (range 5 to 12 alleles per locus) and heterozygosity values at the four disomic loci ranging from 0.46 to 0.66. Multivariate factor analysis of Nei's genetic distance values produced three distinct population groups that were organized by geography: 1) Mattagami (northern Quebec), 2) Menominee/ Wolf (Lake Michigan - Wisconsin), and 3) St. Lawrence/ Des Prairies/ Niagara/ Erie (lower Great Lakes). Differences based on G-tests summed over all loci occurred between all possible paired comparisons of the collections (P < 0.01). These analyses indicated that lake sturgeon populations are differentiated within the Great Lakes basin. Managers of this species will need to identify individual populations in their jurisdictions and provide separate consideration for their conservation and rehabilitation.

Journal of Great Lakes Research↗

USGS2017

Spatial and temporal genetic analysis of Walleyes in the Ohio River

Previous genetic analyses have shown that Walleyes Sander vitreus in the upper Ohio River comprise two distinct genetic strains: (1) fish of Great Lakes origin that were stocked into the Ohio River basin and (2) a remnant native strain (Highlands strain). Resource agencies are developing management strategies to conserve and restore the native strain within the upper reaches of the Ohio River. Hybridization between strains has impacted the genetic integrity of the native strain. To better understand the extent and effects of hybridization on the native strain, we used mitochondrial DNA and microsatellite markers to evaluate the spatial (river sections) and temporal (pre- and poststocking) genetic diversity of Ohio River Walleyes. Contemporary Lake Erie Walleyes and archival museum specimens collected from the Ohio River basin were used for comparison to contemporary Ohio River samples. Although there was evidence of hybridization between strains, most of the genetic diversity within the Ohio River was partitioned by basin of origin (Great Lakes versus the Ohio River), with greater similarity among river sections than between strains within the same section. Results also suggested that the native strain has diverged from historical populations. Furthermore, notable decreases in measures of genetic diversity and increased relatedness among native-strain Walleyes within two sections of the Ohio River may be related to stocking aimed at restoration of the Highlands strain. Our results suggest that although the Highlands strain persists within the Ohio River, it has diverged over time, and managers should consider the potential impacts of future management practices on the genetic diversity of this native strain.

Ohio River↗

USGS2013

Conservation in an age of climate change

Are you a gardener? Then you know that certain species and varieties of species grow best in certain growing zones related to climate. This growing zone concept also applies to species in natural ecosystems. One threat of climate change to wetland biodiversity is that some species may be losing the ability to track an appropriate season for flowering, seed production and growth, impairing their ability to regenerate. Based on genetic constraints, such species may have a limited ability to adjust to changing climates. For biodiversity conservation to be successful in the future, the first order of business is to formulate the goals of such projects regardless of philosophical differences in approaches. If the real goal is to conserve species, then conservation planners may need to put all management options on the table. Despite the uncertainties, with the risk of species losses so imminent, the best strategy may be to throw any dogmatism out the window and use multiple approaches.

National Wetlands Newsletter↗

USGS1995

Biodiversity: a new challenge

Resource managers at many state and federal agencies are in the middle of a fundamental change in the practice and objectives of conservation. Traditional management has been directed toward maintaining, usually for harvest purposes, populations of individual species such as ducks, deer, or salmon. Increasingly, however, resource managers are recognizing the critical important of conserving biological diversity, or biodiversity. In its simplest terms, biological diversity is the variety of life at all levels: it includes the array of plants and animals; the genetic differences among individuals; the communities, ecosystems, and landscapes in which they occur; and the variety of processes on which they depend. Conserving biological diversity poses dramatic new problems for comprehensive inventory and monitoring: what should be measured or monitored?

Book chapter↗

USGS2013

A network extension of species occupancy models in a patchy environment applied to the Yosemite toad ( Anaxyrus canorus )

A central challenge of conservation biology is using limited data to predict rare species occurrence and identify conservation areas that play a disproportionate role in regional persistence. Where species occupy discrete patches in a landscape, such predictions require data about environmental quality of individual patches and the connectivity among high quality patches. We present a novel extension to species occupancy modeling that blends traditionalpredictions of individual patch environmental quality with network analysis to estimate connectivity characteristics using limited survey data. We demonstrate this approach using environmental and geospatial attributes to predict observed occupancy patterns of the Yosemite toad ( Anaxyrus (= Bufo) canorus ) across >2,500 meadows in Yosemite National Park (USA). A. canorus , a Federal Proposed Species, breeds in shallow water associated with meadows. Our generalized linear model (GLM) accurately predicted ~84% of true presence-absence data on a subset of data withheld for testing. The predicted environmental quality of each meadow was iteratively ‘boosted’ by the quality of neighbors within dispersal distance. We used this park-wide meadow connectivity network to estimate the relative influence of an individual Meadow’s ‘environmental quality’ versus its ‘network quality’ to predict: a) clusters of high quality breeding meadows potentially linked by dispersal, b) breeding meadows with high environmental quality that are isolated from other such meadows, c) breeding meadows with lower environmental quality where long-term persistence may critically depend on the network neighborhood, and d) breeding meadows with the biggest impact on park-wide breeding patterns. Combined with targeted data on dispersal, genetics, disease, and other potential stressors, these results can guide designation of core conservation areas for A. canorus in Yosemite National Park.

California↗

USGS2016

Addressing potential local adaptation in species distribution models: implications for conservation under climate change

Species distribution models (SDMs) have been criticized for involving assumptions that ignore or categorize many ecologically relevant factors such as dispersal ability and biotic interactions. Another potential source of model error is the assumption that species are ecologically uniform in their climatic tolerances across their range. Typically, SDMs to treat a species as a single entity, although populations of many species differ due to local adaptation or other genetic differentiation. Not taking local adaptation into account, may lead to incorrect range prediction and therefore misplaced conservation efforts. A constraint is that we often do not know the degree to which populations are locally adapted, however. Lacking experimental evidence, we still can evaluate niche differentiation within a species' range to promote better conservation decisions. We explore possible conservation implications of making type I or type II errors in this context. For each of two species, we construct three separate MaxEnt models, one considering the species as a single population and two of disjunct populations. PCA analyses and response curves indicate different climate characteristics in the current environments of the populations. Model projections into future climates indicate minimal overlap between areas predicted to be climatically suitable by the whole species versus population-based models. We present a workflow for addressing uncertainty surrounding local adaptation in SDM application and illustrate the value of conducting population-based models to compare with whole-species models. These comparisons might result in more cautious management actions when alternative range outcomes are considered.

Ecological Applications↗

USGS2022

Genetic analyses provide new insight on the mating strategies of the American Black Swift (Cypseloides niger)

Avian mating strategies play a vital role in the demographic and genetic dynamics of a species and understanding avian reproductive tactics is important to conservation, population management and restoration. Classifications of avian mating strategies have historically been based on direct physical observations and tend to be rigid population-level generalizations that overlook the variations inherent in most ecological systems. Based on limited empirical field observations, the American Black Swift Cypseloides niger borealis is considered to be a socially monogamous species with pair bonds lasting for many years. To test this hypothesis, we collected genomic DNA samples from banded swifts from six American Black Swift colonies in the western United States from 2004 to 2019 and isolated and developed primers for highly polymorphic microsatellite loci and used them to genotype our samples. Our parentage analysis revealed that sampled females never mated with the same male in subsequent years, suggesting that they are not sexually monogamous with a single partner for many years as previously hypothesized.

Colorado, Idaho, New Mexico↗

USGS1997

Characterization and application of a quantitative DNA marker that discriminates sex in chinook salmon (Oncorhynchus tshawytscha)

A qualitative male-specific DNA marker (OT-24) was amplified by spPCR (single-primer polymerase chain reaction) from chinook salmon (Oncorhynchus tshawytscha) DNA along with several non-sex-linked products. The termini of the male-specific product were sequenced, and a pair of PeR primers were constructed for marker-specific PCR amplification. Dual primer PCR (dpPCR), with the marker-specific primers, amplified a product from both nudes and females. The amount of dpPCR product amplified from males was at least 100-fold greater than that from females. The quantitative difference between males and females was consistent among geographically distinct populations from western U.S. rivers. In addition, DNA sequence analysis indicated that OT-24 was highly conserved among geographically distinct salmon populations. The qualitative spPCR product segregated through several genetic crosses indicating equal sex ratios among progeny. Identification of the male and female juveniles by dpPCR was consistent with the spPCR analysis. There was no tissue specificity observed by spPCR or dpPCR analysis of this marker. A rapid DNA extraction method and dpPCR analysis were used to nonlethally determine sex ratios in wild spring chinook salmon adults, withheld for genetic and behavioral studies, prior to their development of gross sexual differences in their external morphology.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS1997

Characterization and application of a quantitative DNA marker that discriminates sex in Chinook salmon ( Oncorhynchus tshawytscha )

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2005

Genetics of Central Valley, O. mykiss, populations: Drainage and watershed scale analyses

Genetic variation at 11 microsatellite loci described population genetic structure for Oncorhynchus mykiss in the Central Valley, California. Spatial and temporal variation was examined as well as relationships between hatchery and putative natural spawning anadromous stocks. Genetic diversity was analyzed at two distinct spatial scales: fine-scale within drainage for five populations on Clear Creek; between and among drainage diversity for 23 populations. Significant regional spatial structure was apparent, both within Clear Creek and among rainbow trout populations throughout the Central Valley. Significant differences in allelic frequencies were found among most river or drainage systems. Less than 1% of the molecular variance could be attributed to differences found between drainages. Hatchery populations were shown to carry similar genetic diversity to geographically proximate wild populations. Central Valley M = 0.626 (below the M < 0.68 threshold) supported recent population reductions within the Central Valley. However, average estimated effective population size was relatively high (Ne = 5066). Significant allelic differences were found in rainbow trout collected above and below impassable dams on the American, Yuba, Stanislaus and Tuolumne rivers. Rainbow trout sampled in Spring Creek were extremely bottlenecked with allelic variation at only two loci and an estimated effective population size of 62, suggesting some local freshwater O. mykiss stocks may be declining rapidly. These data support significant genetic population structure for steelhead and rainbow trout populations within the Central Valley across multiple scales. Careful consideration of this genetic diversity and its distribution across the landscape should be part of future conservation and restoration efforts.

California↗

USGS2023

Host vs. pathogen evolutionary arms race: Effects of exposure history on individual response to a genetically diverse pathogen

Introduction: Throughout their range, bighorn sheep ( Ovis canadensis ) populations have seen significant disease-associated declines. Unfortunately, understanding of the underlying epidemiological processes driving the disease dynamics in this species has hindered conservation efforts aimed at improving the health and long-term viability of these populations. Individual response to pathogen exposure emerges from dynamic interactions between competing evolutionary processes within the host and pathogen. The host’s adaptive immune system recognizes pathogens and mounts a defensive response. Pathogens have evolved strategies to overcome adaptive immune defenses including maintaining high genetic diversity through rapid evolution. The outcomes of this evolutionary warfare determine the success of pathogen invasion of the host and ultimately the success of conservation efforts. Methods: During an epizootic dominated by a single strain, we explore these host-pathogen dynamics by examining the variation in effects of pathogen invasion on captive bighorn sheep with differing histories of exposure to genetically diverse strains of Mycoplasma ovipneumoniae (Movi). We monitored clinical signs of disease and sampled animals and their environment to detect spread of Movi among 37 bighorn sheep separated into nine pens based on known exposure Results: We documented Movi transmission within and across pens and we detected Movi DNA in air, water, and invertebrate samples. Higher levels of antibody to Movi prior to the epizootic were associated with a lower likelihood of presenting clinical signs of pneumonia. Nonetheless, higher antibody levels in symptomatic individuals were associated with more severe progressive disease, increased probability and speed of pneumonia-induced mortality, and reduced likelihood of returning to a healthy state. Bighorn sheep with previous exposure to a strain other than the predominant epizootic strain were more likely to recover. Discussion: Our results indicate that Movi-strain variability was sufficient to overwhelm the adaptive host immunological defenses. This outcome indicates, in free-ranging herds, past exposure is likely insufficient to protect bighorn sheep from infection by new Movi strains, although it influences the progression of disease and recovery within the herd. Therefore, given Movi-strain variability and the lack of immunological protection from past exposure, focusing management efforts on minimizing the introduction of Movi into bighorn herds, through separation of domestic and bighorn sheep and avoidance of management activities that create commingling of bighorn sheep carrying differing Movi strains, will likely be the most effective approach for reducing the effects of disease and achieving bighorn sheep conservation goals.

Idaho, Oregon, South Dakota, Washington↗

USGS2019

Genetic mark‐recapture analysis of winter faecal pellets allows estimation of population size in Sage Grouse Centrocercus urophasianus

The Sage Grouse Centrocercus urophasianus is a species of conservation concern throughout its range in western North America. Since the 1950s, the high count of males at leks has been used as an index for monitoring populations. However, the relationship between this lek‐count index and population size is unclear, and its reliability for assessing population trends has been questioned. We used non‐invasive genetic mark‐recapture analysis of faecal and feather samples to estimate pre‐breeding population size for the Parachute‐Piceance‐Roan, a small, geographically isolated population of Sage Grouse in western Colorado, during two consecutive winters from 2012 to 2014. We estimated total pre‐breeding population size as 335 (95% confidence interval (CI): 287–382) in the first winter and 745 (95% CI: 627–864) in the second, an approximate doubling in abundance between years. Although we also observed a large increase in the spring lek‐count index between those years, high male count data poorly represented mark‐recapture estimates of male abundance in each year. Our data suggest that lek counts are useful for detecting the direction and magnitude of large changes in Sage Grouse abundance over time but they may not reliably reflect small changes in abundance that may be relevant to small populations of conservation concern.

Colorado↗

USGS2012

A fine-scale assessment of using barriers to conserve native stream salmonids: a case study in Akokala Creek, Glacier National Park, USA

Biologists are often faced with the difficult decision in managing native salmonids of where and when to install barriers as a conservation action to prevent upstream invasion of nonnative fishes. However, fine-scale approaches to assess long-term persistence of populations within streams and watersheds chosen for isolation management are often lacking. We employed a spatially-explicit approach to evaluate stream habitat conditions, relative abundance, and genetic diversity of native westslope cutthroat trout (Oncorhynchus clarkii lewisi) within the Akokala Creek watershed in Glacier National Park- a population threatened by introgressive hybridization with nonnative rainbow trout (O. mykiss) from nearby sources. The systematic survey of 24 stream reaches showed broad overlap in fish population and suitable habitat characteristics among reaches and no natural barriers to fish migration were found. Analysis of population structure using 16 microsatellite loci showed modest amounts of genetic diversity among reaches, and that fish from Long Bow Creek were the only moderately distinct genetic group. We then used this information to assess the potential impacts of three barrier placement scenarios on long-term population persistence and genetic diversity. The two barrier placement scenarios in headwater areas generally failed to meet general persistence criteria for minimum population size (2,500 individuals, Ne = 500), maintenance of long-term genetic diversity (He), and no population subdivision. Conversely, placing a barrier near the stream mouth and selectively passing non-hybridized, migratory spawners entering Akokala Creek met all persistence criteria and may offer the best option to conserve native trout populations and life history diversity. Systematic, fine-scale stream habitat, fish distribution, and genetic assessments in streams chosen for barrier installation are needed in conjunction with broader scale assessments to understand the potential impacts of using barriers for conservation of native salmonid populations threatened by nonnative fish invasions.

Open Fish Science Journal↗

USGS2012

Emerging prion disease drives host selection in a wildlife population

Infectious diseases are increasingly recognized as an important force driving population dynamics, conservation biology, and natural selection in wildlife populations. Infectious agents have been implicated in the decline of small or endangered populations and may act to constrain population size, distribution, growth rates, or migration patterns. Further, diseases may provide selective pressures that shape the genetic diversity of populations or species. Thus, understanding disease dynamics and selective pressures from pathogens is crucial to understanding population processes, managing wildlife diseases, and conserving biological diversity. There is ample evidence that variation in the prion protein gene (PRNP) impacts host susceptibility to prion diseases. Still, little is known about how genetic differences might influence natural selection within wildlife populations. Here we link genetic variation with differential susceptibility of white-tailed deer to chronic wasting disease (CWD), with implications for fitness and disease-driven genetic selection. We developed a single nucleotide polymorphism (SNP) assay to efficiently genotype deer at the locus of interest (in the 96th codon of the PRNP gene). Then, using a Bayesian modeling approach, we found that the more susceptible genotype had over four times greater risk of CWD infection; and, once infected, deer with the resistant genotype survived 49% longer (8.25 more months). We used these epidemiological parameters in a multi-stage population matrix model to evaluate relative fitness based on genotype-specific population growth rates. The differences in disease infection and mortality rates allowed genetically resistant deer to achieve higher population growth and obtain a long-term fitness advantage, which translated into a selection coefficient of over 1% favoring the CWD-resistant genotype. This selective pressure suggests that the resistant allele could become dominant in the population within an evolutionarily short time frame. Our work provides a rare example of a quantifiable disease-driven selection process in a wildlife population, demonstrating the potential for infectious diseases to alter host populations. This will have direct bearing on the epidemiology, dynamics, and future trends in CWD transmission and spread. Understanding genotype-specific epidemiology will improve predictive models and inform management strategies for CWD-affected cervid populations.

Ecological Applications↗

USGS2017

Evolutionary dynamics of an expressed MHC class IIβ locus in the Ranidae (Anura) uncovered by genome walking and high-throughput amplicon sequencing

The Major Histocompatibility Complex (MHC) is a genomic region encoding immune loci that are important and frequently used markers in studies of adaptive genetic variation and disease resistance. Given the primary role of infectious diseases in contributing to global amphibian declines, we characterized the hypervariable exon 2 and flanking introns of the MHC Class IIβ chain for 17 species of frogs in the Ranidae, a speciose and cosmopolitan family facing widespread pathogen infections and declines. We find high levels of genetic variation concentrated in the Peptide Binding Region (PBR) of the exon. Ten codons are under positive selection, nine of which are located in the mammal-defined PBR. We hypothesize that the tenth codon (residue 21) is an amphibian-specific PBR site that may be important in disease resistance. Trans-species and trans-generic polymorphisms are evident from exon-based genealogies, and co-phylogenetic analyses between intron, exon and mitochondrial based reconstructions reveal incongruent topologies, likely due to different locus histories. We developed two sets of barcoded adapters that reliably amplify a single and likely functional locus in all screened species using both 454 and Illumina based sequencing methods. These primers provide a resource for multiplexing and directly sequencing hundreds of samples in a single sequencing run, avoiding the labour and chimeric sequences associated with cloning, and enabling MHC population genetic analyses. Although the primers are currently limited to the 17 species we tested, these sequences and protocols provide a useful genetic resource and can serve as a starting point for future disease, adaptation and conservation studies across a range of anuran taxa.

Developmental and Comparative Immunology↗

USGS2023

Using genetic data to advance stream fish reintroduction science: A case study in brook trout

Widespread extirpation of native fish populations has led to a rise in species reintroduction efforts worldwide. Most efforts have relied on demographic data alone to guide project design and evaluate success. However, the genetic characteristics of many imperiled fish populations including low diversity, local adaptation, and hatchery introgression emphasize the importance of genetic data in the design and monitoring of reintroduction efforts. Focusing on a case study of brook trout ( Salvelinus fontinalis ) in North Carolina, USA, we show how the combined use of genetic and demographic data can support reintroduction efforts by improving source population selection and providing opportunities to evaluate genetic viability and adaptive potential in restored populations. Using this combined approach, we reintroduced brook trout into a restored stream from two source populations and monitored changes in genetic diversity and population size in source and recipient populations. Three years after the initial translocation, the reintroduced population had comparable density, but higher genetic diversity, than either source population. This study demonstrates the utility of genetic and demographic data for reintroduction efforts, particularly when extant populations are genetically depauperate and maintaining adaptive potential is a primary restoration goal. However, we emphasize the value of continued monitoring at longer temporal and spatial scales to determine the effects of stochastic process on the long-term adaptive capacity and persistence of reintroduced populations. Overall, inclusion of genetic data in reintroduction efforts offers increased ability to meet project goals while simultaneously conserving critical sources of adaptive variation that exist across the landscape.

North Carolina↗